STAR mapping issue

[salim...@gmail.com]

Hi all, 

I am trying to run STAR on some sample on a server and while it seems to run just fine I am facing 2 issues which I actually think is only one.  While the mapping is running I always get the same line : --outFileNamePrefix: command not found. 

The weird thing is that STAR keep running and creating the directory for each sample that I have in the bash script. However, the directory stays empty and the log.out files are stored in the current directory instead of being stored in the directory that I created. Also, when i let it run through all the samples the log.final.out keep changing in term of reads mapped and so on probably because it is overwriting the file over and over....Has anyone had the same problem before ? 

Many thanks, 

Salim. 

[Ramakrishnan]

Salim,

1. you are missing a backslash (\) on line 7 of your script.

2. the prefix should either be a <path to a directory> or a <string> that will be prefixed to all STAR outputs. See section 4 of the manual.

Best

Ram

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Dr. Ramakrishnan Natesan
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Department of Cancer Biology
University of Pennsylvania
Philadelphia

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